Chemistry is an important subject due to understanding the composition and structure of the things around us. The main aim of the study was to find out the perception of chemistry by lower secondary school pupils. The partial aims were to find out the influence of gender, year of study and favorite subject on the perception of chemistry. The sample size comprised 379 Czech lower secondary schools pupils. The questionnaire was used as a research tool. It consisted of 25 5-point Likert type items. Items were, after application of factor analysis, divided into four categories: (1) The interest in chemistry, (2) The relevance of chemistry, (3) The future life and chemistry, and (4) Chemical aids and laboratory experiments. Reliability of the research tool was determined by Cronbach's alpha which had value a = 0.87). For the data evaluation the methods of inferential statistics were used, concretely analysis of variance (ANOVA). Pupils had low positive perception of chemistry. Statistically significant differences between boys and girls and also between 8th and 9th graders were not found out. In the conclusion part the possibilities of next research and also recommendations for practice are presented.